BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations

There is an accelerating interest in practical applications of alchemical free energy methods to problems in protein design, constant pH simulations, and especially computer-aided drug design. In the present paper, we describe a basic lambda dynamics engine (BLaDE) that enables alchemical free energy simulations, including multisite lambda dynamics (MS lambda D) simulations, on graphical processor units (GPUs). We find that BLaDE is 5 to 8 times faster than the current GPU implementation of MS lambda D-based free energy calculations in CHARMM. We also demonstrate that BLaDE running standard molecular dynamics attains a performance competitive with and sometimes exceeding that of the highly optimized OpenMM GPU code. BLaDE is available as a standalone program and through an API in CHARMM.

Automated summary

This paper introduces a basic Lambda dynamics engine called BLaDE, which allows for alchemical free energy simulations on GPUs and is faster than current GPU implementations. Research shows that BLaDE's performance in standard molecular dynamics is competitive with the highly optimized OpenMM GPU code.